Mesoscopic analysis of conformational and entropic contributions to nonspecific adsorption of HP copolymer chains using dynamic Monte Carlo simulations

Dynamic Monte Carlo simulations of short linear HP-type copolymers exhibiting proteinlike characteristics are used to investigate both chain dynamics and changes in chain conformational entropy and their contributions to the energetics of adsorption onto a solid-liquid interface. The dMC results show that the conformations and energies of adsorbed chains are highly degenerate. The ensemble-averaged energy of the adsorbed state is dependent on temperature, chain sequence, native-state stability, and sorbent surface geometry and hydrophobicity. Mesoscopic thermodynamic analyses reveal that, although increased chain conformational entropy contributes to the driving force for adsorption in certain cases, many conditions exist where the change in conformational entropy is either negligible or unfavorable due to constraints imposed by the need to form a large and specific number of favorable intra- and intermolecular contacts and by the impenetrable nature of the sorbent surface. Step-number-averaged energy trajectories, based on sampling of a large number of energy trajectories and thus conformational states at each step number, suggest that the search for a global energy minimum is gradual, so that adsorption is first reversible but becomes apparently irreversible with longer exposure to the sorbent. These results appear to be connected to the conformational adaptability of the chain both on the surface and in solution, and an adsorption model taking chain conformational dynamics into account is proposed.     

Lattice Monte Carlo simulations of three-dimensional charged polymer chains

The configurational properties of strongly charged polyelectrolytes accompanied by neutralizing counterions in dilute solutions are simulated using the cooperative motion algorithm on the face-centered-cubic lattice. The full Coulomb potential and the excluded volume condition between different ions/beads are taken into account and the reduced temperature T* is considered the main, variable parameter. The calculations that have been carried out for solutions of both single and several chains indicate a few regions of their behavior: (1) for T*--> infinity, it corresponds to that of neutral, self-avoiding polymers under good solvent conditions; (2) for T* approximately 1, due to the electrostatic interactions being effectively stronger, the chains are more outstretched compared to their size at other temperatures; (3) for T* well below one, the counterion condensation becomes more and more dominant, which gradually leads to strongly collapsed chains; and (4) at the lowest temperatures the chains and counterions assume low-energy configurations in the form of neutral, compact aggregates.     

Monte Carlo simulations of chains confined inside a cube

Self-avoiding walks (SAWs) and random-flight walks (RFWs) of various lengths embedded on a simple cubic lattice have been computer generated inside cubes of varying side. If B is the side of the confining cube, we define the reduced cube side size B₀ as B₀ = (B − 1)/<r²>^1/2, where <r²>^1/2 is the root-mean-square end-to-end distance of the non-confined chains. Dimensionless diagrams are then given of the Monte Carlo estimates for the dimensions, the entropy, and the compressibility parameter PV/(kT) of the confined chains as a function of B₀. The comparative behaviour of the confined SAWs and RFWs is established, scaling properties are examined, and the Monte Carlo estimates compared with theory when such theory is available.     

Three-dimensional dynamic Monte Carlo simulations of elastic actin-like ratchets

We present three-dimensional dynamic Monte Carlo simulations of the growth of a semiflexible fiber against a fluctuating obstacle. The natural reference for our numerical study are the elastic and Brownian ratchet models previously analyzed semianalytically. We find that the decay of the velocity versus applied load is exponential to a good degree of accuracy, provided we include in the load the drag force felt by the moving obstacle. If the fiber and obstacle only interact via excluded volume, there are small corrections to the Brownian ratchet predictions which suggest that tip fluctuations play a minor role. If on the other hand fiber and obstacle interact via a soft potential, the corrections are much larger when the obstacle diffuses slowly. This means that microscopic assumptions can profoundly affect the dynamics. We also identify and characterize a novel "pushing catastrophe"--which is distinct from the usual fiber buckling--in which the growth of the fiber decouples from the obstacle movement. The time distribution of catastrophes can be explained via an approximate analytical treatment, and our numerics suggest that the time taken to lose propulsive force is largely dependent on the fiber incidence angle. Our results are a first step in realizing numerical polymer models for the motion of sets or networks of semiflexible fibers close to a fluctuating membrane or obstacle.     

Irreversible adsorption of tethered chains at substrates: Monte Carlo study

The irreversible adsorption of single chains grafted with one end to the surface is studied using scaling arguments and computer simulations. We introduce a two-phase model, in which the chain is described by an adsorbate portion and a corona portion formed by nonadsorbed monomers. The adsorption process can be viewed as consisting of a main stage, during which monomers join by "zipping" (along their order in the chain) the surface, and a late stage, in which the remaining corona collapses on the surface. Based on our model we derive a scaling relation for the time of adsorption t(M) as a function of the number M of adsorbed monomers; t(M) follows a power law, M(alpha), with alpha > 1. We find that alpha is related to the Flory exponent nu by alpha = 1 + nu. Using further scaling arguments we derive relations between the overall time of adsorption, the characteristic time of adsorption (given by the crossover time between the main and the last stage of adsorption), and the chain length. To support our analysis we perform Monte Carlo simulations using the bond fluctuation model. In particular, the sequence of adsorption events is very well reproduced by the simulations, and an analysis of the various density profiles supports our theoretical model. Especially the loop formation during adsorption clearly shows that the growth of the adsorbate is dominated by zipping. The simulations are also in almost quantitative agreement with our theoretical scaling analysis, showing that here the assumption of a linear relation between Monte Carlo steps and time is well obeyed. We conclude by also discussing the geometrical shape of the adsorbate.     

Monte Carlo simulations of hydrogen adsorption in alkali-doped single-walled carbon nanotubes

Monte Carlo simulations and Widom's test particle insertion method have been used to calculate the solubility coefficients (S) and the adsorption equilibrium constants (K) in single-walled (10,10) armchair carbon nanotubes including single nanotubes, and nanotube bundles with various configurations with and without alkali dopants. The hydrogen adsorption isotherms at room temperature were predicted by following the Langmuir adsorption model using the calculated constants S and K. The simulation results were in good agreement with experimental data as well as the grand canonical Monte Carlo simulation results reported in the literature. The simulations of nanotube bundle configurations suggest that the gravimetric hydrogen adsorption increases with internanotube gap size. It may be attributed to favorable hydrogen-nanotube interactions outside the nanotubes. The effect of alkali doping on hydrogen adsorption was studied by incorporating K+ or Li+ ions into nanotube arrays using a Monte Carlo simulation. The results on hydrogen adsorption isotherms indicate hydrogen adsorption of 3.95 wt% for K-doping, and 4.21 wt% for Li-doping, in reasonable agreement with the experimental results obtained at 100 atm and room temperature.     

Monte Carlo simulations of antibody adsorption and orientation on charged surfaces

Monte Carlo simulations were performed to study the adsorption and orientation of antibodies on charged surfaces based on both colloidal and all-atom models. The colloidal model antibody consists of 12 connected beads representing the 12 domains of an antibody molecule. The structure of the all-atom antibody model was taken from the protein databank. The effects of the surface charge sign and density, the solution pH and ionic strength on the adsorption and orientation of different colloidal model antibodies with different dipole moments were examined. Simulation results show that both the 12-bead and the all-atom models of the antibody, for which the dipole moment points from the Fc to (Fab)2 fragments, tend to have the desired "end-on" orientation on positively charged surfaces and undesired "head-on" orientation on negatively charged surfaces at high surface charge density and low solution ionic strength where electrostatic interactions dominate. At low surface charge density and high solution ionic strength where van der Waals interactions dominate, 12-bead model antibodies tend to have "lying-flat" orientation on surfaces. The orientation of adsorbed antibodies results from the compromise between electrostatic and van der Waals interactions. The dipole moment of an antibody is an important factor for antibody orientation on charged surfaces when electrostatic interactions dominate. This charge-driven protein orientation hypothesis was verified by our simulations results in this work. It was further confirmed by surface plasmon resonance biosensor and time-of-flight secondary ion mass spectrometry experiments reported elsewhere.     

Monte Carlo simulations on the effect of substrate geometry on adsorption and compression

Canonical Monte Carlo simulations were used to study the adsorption and compression of fluid layers on model substrates with cubic, (111) fcc, and graphite geometries. The effect of the relative size of the fluid and substrate molecules on adsorption was considered for strong molecule-surface interactions. In the case of monolayer formation, it was found that the surface geometry and the size of the adsorbate molecules had a significant effect on the structure of the adsorbed layer. These structures varied from well-ordered, commensurate layers to liquid-like structures. Lateral compression was observed for certain fluid to substrate molecule sizes. For the interactions studied in this work, it was found that maximum lateral compression occurred on the cubic surface when adsorbate molecules had a diameter approximately 15% larger than the substrate diameter. In the case of multilayer formation, it was found that second and higher adsorbed layers could compress into the adsorbed layers below them. For cubic substrates, the interlayer compression was predicted analytically with reasonable accuracy, with maximum interlayer compression found for fluid diameters approximately 90% the size of substrate molecule diameters.     

Mesoscopic Monte Carlo simulations of stochastic encounters between photoactivated rhodopsin and transducin in disc membranes

The issue of how the molecular organization of rod outer segments (ROS) discs affects the initial timing of the photoresponse in vertebrates has been recently raised by novel structural findings that raise doubts about the classical scenario of monomeric rhodopsin (R) and heterotrimeric transducin (G) freely diffusing in the membrane milieu. In this study, we investigate this issue by means of mesoscopic Monte Carlo (MMC) simulations of the stochastic encounters between one photoactivated R and one G, explicitly taking into account the molecular size and the diffusion coefficient of each species as well as crowding effects. Three different scenarios were compared with respect to their effects on timing, namely, (a) the classical framework, where both G and monomeric R are allowed to freely diffuse in the ROS disc membrane, (b) the ideal paracrystalline organization of R dimers considered as a structural unit, where ordered rows completely cover the disc membrane patch, and (c) the scenario suggested by recent AFM data, where R dimers organize in differently sized rafts with varying local concentrations. Our simulations suggest that a similar kinetic response could arise from very different microscopic scenarios, thus opening new interpretations to the controversial recent findings. Moreover, we show that if high-density R packing on ROS discs is characterized by a highly ordered structural organization rather than unspecific aggregation, an unexpected favorable effect on the temporal response of early phototransduction reactions can occur.     

Extensional flow of bulk polymers studied by dynamic Monte Carlo simulations

Dynamic Monte Carlo simulations of bulk lattice polymers driven through planar geometries with sequentially converging,parallel and diverging spaces between two neutrally repulsive solid plates are reported.The spatial profiles of polymer velocity and deformation along the course of such a laminar extensional flow have been carefully analyzed.The results appear consistent with experimental observations in literature.In the entrance and exit regions,a linear dependence of chain extension upon the excess velocity has been observed.Moreover,an annexed shear flow and a molecular-dispersion effect are found.The results demonstrate a useful strategy of this approach to study polymer flows and bring new insights into the non-Newtonian-fluid behaviors of bulk polymers in capillary rheometers and micro-fluidic devices.     

Monte Carlo simulations of Lennard-Jones nonionic surfactant adsorption at the liquid/vapor interface

We present Monte Carlo simulations of nonionic surfactant adsorption at the liquid/vapor interface of a monatomic solvent. All molecules in the system, solvent and surfactant, are characterized by the Lennard-Jones (LJ) potential using differing interaction parameters. Surfactant molecules consist of an amphiphilic chain with a solvophilic head and a solvophobic tail. Adjacent atoms along the surfactant chain are connected by finitely extensible harmonic springs. Solvent molecules move via the Metropolis random-walk algorithm, whereas surfactant molecules move according to the continuum configurational bias Monte Carlo (CBMC) method. We generate quantitative thermodynamic adsorption and surface tension isotherms in addition to surfactant radius of gyration, tilt angles, and potentials of mean force. Surface tension simulations compared to those calculated from the simulated adsorbed amounts and the Gibbs adsorption isotherm agree confirming equilibrium in our simulations. We find that the classical Langmuir isotherm is obeyed for our LJ surfactants over the range of head and tail lengths studied. Although simulated surfactant chains in the bulk solution exhibit random orientations, surfactant chains at the interface orient roughly perpendicular and the tails elongate compared to bulk chains even in the submonolayer adsorption regime. At a critical surfactant concentration, designated as the critical aggregation concentration (CAC), we find aggregates in the solution away from the interface. At higher concentrations, simulated surface tensions remain practically constant. Using the simulated potential of mean force in the submonolayer regime and an estimate of the surfactant footprint at the CAC, we predict a priori the Langmuir adsorption constant, KL, and the maximum monolayer adsorption, Gammam. Adsorption is driven not by proclivity of the surfactant for the interface, but by the dislike of the surfactant tails for the solvent, that is by a "solvophobic" effect. Accordingly, we establish that a coarse-grained LJ surfactant system mimics well the expected equilibrium behavior of aqueous nonionic surfactants adsorbing at the air/water interface.     

Monte Carlo studies of tethered chains

Monte Carlo computer simulations of end-tethered chains grafted onto a hard wall have been performed. The chains were modeled as self-avoiding chains on a cubic lattice at athermal solvent conditions. The simulations spanned a wide range of chain lengths, N (100–1000, i.e., up to molecular weights of a few hundred thousands), and anchoring densities, σ (2 × 10⁻⁴ to 0.4), to properly chart the relevant parameter space. It is shown that the reduced surface coverage σ* = σπR is the most appropriate variable that quantitatively determines the mushroom, overlapping mushroom and brush regimes, where R_g is the radius of gyration of a free chain in solution. The simulation data are analyzed to determine the conformational characteristics and shape of the anchored chains and to compare them with the predictions of the analytical self consistent field theory. The strong stretching limit of the theoretical predictions is obtained only for σ* > 8. © 2009 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 47:2449–2461, 2009     

Monte Carlo simulations of phase transitions and adsorption isotherm discontinuities on surface compression

Low temperature, Grand Canonical Monte Carlo simulations were used to study the adsorption of fluid layers on cubic, hexagonal, and atomically smooth substrates to determine the effects of registry and surface compression on the system. The size of the fluid molecules was fixed to be 20% larger than the substrate molecules in order to observe the transition from an expanded to commensurate and finally to an incommensurate monolayer. For relatively weak fluid-substrate interactions, the cubic system underwent a first-order phase transition. As the strength of the fluid-substrate interactions increased, the molecules became fixed at commensurate locations and the transition from low density to commensurate packing became continuous. The strong fluid-substrate interactions lead to the development of a kink in the adsorption isotherm that showed the increased stability of the commensurate phase. This kink became more pronounced as the system temperature was decreased. The hexagonal system showed less dramatic results due to a decrease in the substrate well depth of the relative to the cubic system. The system did experience a first-order phase transition for a weak fluid-substrate interactions and the transition became much more gradual as the fluid-substrate interaction increased. The molecules became fixed to commensurate substrate locations, but the surface was not corrugated sufficiently to have a stable commensurate phase. The atomically smooth substrate showed the first-order phase transition expected of a low temperature system with no effects of registry.     

Confined crystallization of cylindrical diblock copolymers studied by dynamic Monte Carlo simulations

We report dynamic Monte Carlo simulations of polymer crystallization confined in the cylindrical microdomains of diblock copolymers. The microdomains were prepared via spontaneous microphase separation from homogeneous melt, and the major component was then frozen in a vitreous amorphous state to make a hard confinement to the crystallization of the minor component. We found that during the isothermal crystallization at high temperatures, crystal orientations are dominantly perpendicular to the cylinder axis at the early stage of crystal nucleation and remain to the final state; while if the block junctions are broken before crystallization, crystal orientations are dominantly parallel at the early stage of crystal nucleation, and eventually other orientations take the place of parallel preferences. Analysis of bond orientations in the heterogeneous melts demonstrates the microscopic origin of oriented crystal nucleation.     

Lattice Monte Carlo simulations of three-dimensional charged polymer chains. II. Added salt

The configurational properties of strongly charged polyelectrolytes accompanied by counterions and salt ions in dilute solutions are simulated using the cooperative motion algorithm on the face-centered-cubic lattice. The calculations indicate that both positive and negative ions condense on the chains at sufficiently low temperatures and their amount depends on the concentration of added salt. As the temperature decreases from high to low, the chains undergo conformational changes from neutral-like, self-avoiding polymers by more outstretched forms to compact globules. The observed extension of the chains at intermediate temperatures is also affected by the amount of salt. Furthermore, configurations with the lowest energies recorded at the lowest temperatures are aggregates of single or more entangled chains and ions of both types.     

Reactive Monte Carlo and grand-canonical Monte Carlo simulations of the propene metathesis reaction system

The influence of silicalite-1 pores on the reaction equilibria and the selectivity of the propene metathesis reaction system in the temperature range between 300 and 600 K and the pressure range from 0.5 to 7 bars has been investigated with molecular simulations. The reactive Monte Carlo (RxMC) technique was applied for bulk-phase simulations in the isobaric-isothermal ensemble and for two phase systems in the Gibbs ensemble. Additionally, Monte Carlo simulations in the grand-canonical ensemble (GCMC) have been carried out with and without using the RxMC technique. The various simulation procedures were combined with the configurational-bias Monte Carlo approach. It was found that the GCMC simulations are superior to the Gibbs ensemble simulations for reactions where the bulk-phase equilibrium can be calculated in advance and does not have to be simulated simultaneously with the molecules inside the pore. The confined environment can increase the conversion significantly. A large change in selectivity between the bulk phase and the pore phase is observed. Pressure and temperature have strong influences on both conversion and selectivity. At low pressure and temperature both conversion and selectivity have the highest values. The effect of confinement decreases as the temperature increases.     

The influence of side chains on the properties of simple model biopolymers: Monte Carlo simulations

A model for the simulation of proteins is introduced which is based on a new set of bond vectors and a new method for modeling the side chains of proteins. The drawbacks of united atoms models are summarized and the motivation for this new model is given. Some preliminary results are shown which shall demonstrate the suitability of the model proposed.     

Study on structure formation of short polyethylene chains via dynamic Monte Carlo simulation

Monte Carlo (MC) simulations of structure formation for short polyethylene chains at low temperature are performed based on a recent developed method that uses coarse-grained chains on a high coordination lattice. Local short-range interactions based on rotational isomeric state (RIS) model and long-range interactions obtained from Lennard–Jones (LJ) potential are introduced during the simulation. Properties evaluated from the simulations are the mean square dimensions, anisotropy of the radius of gyration tensor, local conformation determined by the occupancy of trans state and orientation correlation functions, energy of the system, and chain packing reflected by the pair correlation functions and structure factors. All of these parameters reveal an ordering process that produces an approximation to a hexagonal crystal phase. The hexagonal structure is imposed by the presence of a diamond lattice underlying the high coordination lattice on which the simulation is performed. Folding of the chains in the crystal is mandatory, because they have fully extended lengths in excess of the dimension of the simulated periodic box. Nevertheless, the simulations demonstrate that a high degree of crystallinity can be achieved in reasonable computer time. The simulation technique should be applicable to other choices of periodic boundary conditions that do not affect the results as strongly as in the present case.     

Monte Carlo simulations of the adsorption of CO2 on the MgO(100) surface

The adsorption of CO2 gas on the MgO (100) crystal surface is investigated using grand canonical Monte Carlo simulations. This allows us to obtain adsorption isotherms that can be compared with experiment, as well as to explore the possible formation of monolayers of different densities. Our model calculations agree reasonably well with the available experimental results. We find a "low-density" adsorbed monolayer where each CO2 molecule is bound to two Mg2+ ions on the MgO substrate. We also observe the formation of monolayers of higher density, where some of the CO2 molecules have rotated and tilted to expose additional binding sites. Low-temperature simulations of both the low- and high-density monolayers reveal that these states are very close in energy, with binding energies of approximately 7 kcal/mol at T=5 K. The high-density monolayer given by our model has a density that is significantly less than the reported experimental value. We discuss this discrepancy and offer suggestions for resolving it.